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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ), 'gf_id' => 'HOM05D001212', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001212' ), 'data_identifier' => 'HOM05D001212', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001212', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p06250' => 'bna', 'A02p00810' => 'bna', 'A02p39870' => 'bna', 'A03p04840' => 'bna', 'A03p50700' => 'bna', 'A03p61220' => 'bna', 'A05p36970' => 'bna', 'A06p35980' => 'bna', 'A09p13330' => 'bna', 'A09p15770' => 'bna', 'Aa31LG11G4440' => 'aar', 'Aa31LG2G490' => 'aar', 'Aa31LG3G16080' => 'aar', 'Aa31sc16G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1986' => 'aag', 'Actinidia02058' => 'ach', 'Actinidia02059' => 'ach', 'Actinidia04246' => 'ach', 'Actinidia13210' => 'ach', 'Actinidia14102' => 'ach', 'Actinidia14500' => 'ach', 'Actinidia21910' => 'ach', 'Actinidia22315' => 'ach', 'Ah.10g035690' => 'amhyb', 'Ah.12g052730' => 'amhyb', 'Ah.16g104810' => 'amhyb', 'AL2G12630' => 'aly', 'AL6G21680' => 'aly', 'AL6G36870' => 'aly', 'AL7G19850' => 'aly', 'Aqoxy4G03115' => 'aox', 'Aqoxy7G00492' => 'aox', 'Aqoxy7G03531' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1PI2YG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2J1BD7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4NTH9K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9SCD6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C7XUBI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8MTW4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F096Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KG0R3Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TRGC7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZFW2W7' => 'arhy', 'AT1G62990' => 'ath', 'AT4G32040' => 'ath', 'AT5G11060' => 'ath', 'AT5G25220' => 'ath', 'ATR0594G101' => 'atr', 'ATR0629G063' => 'atr', 'ATR0661G507' => 'atr', 'Atru.chr7.2500' => 'acertr', 'Atru.chr7.260' => 'acertr', 'Atru.chr9.1508' => 'acertr', 'AUR62010576' => 'cqu', 'AUR62012445' => 'cqu', 'AUR62017314' => 'cqu', 'AUR62031570' => 'cqu', 'BcaB01g05492' => 'bca', 'BcaB01g06308' => 'bca', 'BcaB07g31372' => 'bca', 'BcaC02g10409' => 'bca', 'BcaC03g13347' => 'bca', 'BcaC03g17916' => 'bca', 'BcaC04g22461' => 'bca', 'BcaC04g22733' => 'bca', 'BcaC06g31927' => 'bca', 'BcaC09g51993' => 'bca', 'BcaNung01908' => 'bca', 'BcaNung02287' => 'bca', 'BcaNung03131' => 'bca', 'BcaNung03209' => 'bca', 'BcaNung04978' => 'bca', 'BcaNung05514' => 'bca', 'BolC1t00686H' => 'bol', 'BolC2t06440H' => 'bol', 'BolC2t12032H' => 'bol', 'BolC3t13065H' => 'bol', 'BolC4t24455H' => 'bol', 'BolC7t44791H' => 'bol', 'BolC7t46355H' => 'bol', 'BolC9t54495H' => 'bol', 'BolC9t54808H' => 'bol', 'BraA01t00592Z' => 'bra', 'BraA02t05064Z' => 'bra', 'BraA02t08949Z' => 'bra', 'BraA03t09823Z' => 'bra', 'BraA03t15166Z' => 'bra', 'BraA06t26522Z' => 'bra', 'BraA09t36982Z' => 'bra', 'BraA09t37219Z' => 'bra', 'C01p06890' => 'bna', 'C02p04830' => 'bna', 'C02p59760' => 'bna', 'C03p05550' => 'bna', 'C04p29220' => 'bna', 'C04p29240' => 'bna', 'C07p42620' => 'bna', 'C07p59070' => 'bna', 'C09p15830' => 'bna', 'C09p19040' => 'bna', 'CAN.G324.27' => 'can', 'CAN.G518.19' => 'can', 'CAN.G981.55' => 'can', 'CANSAT11G0116' => 'cansat', 'CANSAT21G0356' => 'cansat', 'CANSAT25G1761' => 'cansat', 'CARHR048650' => 'chi', 'CARHR188260' => 'chi', 'CARHR202230' => 'chi', 'CARHR239940' => 'chi', 'Carub.0002s0201' => 'cru', 'Carub.0006s0957' => 'cru', 'Carub.0006s2304' => 'cru', 'Carub.0007s0851' => 'cru', 'Ca_04073_v3' => 'car', 'Ca_13042_v3' => 'car', 'Ca_21612_v3' => 'car', 'CBR_g36337' => 'cbr', 'Cc06_g07410' => 'ccan', 'Cc08_g00210' => 'ccan', 'Cc08_g13810' => 'ccan', 'CDE02G1848' => 'cde', 'CDE03G0178' => 'cde', 'CDE05G1560' => 'cde', 'CDE05G3182' => 'cde', 'CDE06G2022' => 'cde', 'CDE06G2180' => 'cde', 'CDE11G0506' => 'cde', 'CDE11G1006' => 'cde', 'Cfa012080' => 'cfa', 'Cfa020889' => 'cfa', 'Cfa020890' => 'cfa', 'Cfa022860' => 'cfa', 'Cfa024529' => 'cfa', 'Ciclev10008269m.g' => 'ccl', 'Ciclev10008821m.g' => 'ccl', 'Ciclev10021319m.g' => 'ccl', 'CiPaw.07G227100' => 'cil', 'CiPaw.08G008400' => 'cil', 'CiPaw.11G142500' => 'cil', 'CiPaw.12G100100' => 'cil', 'CiPaw.15G181600' => 'cil', 'ClCG01G003250' => 'cla', 'ClCG05G016600' => 'cla', 'ClCG08G013550' => 'cla', 'COL.COLO4_18914' => 'col', 'COL.COLO4_23792' => 'col', 'COL.COLO4_24100' => 'col', 'Cpa.g.sc187.27' => 'cpa', 'Cpa.g.sc29.29' => 'cpa', 'Cpa.g.sc46.88' => 'cpa', 'Cre08.g375400' => 'cre', 'CsaV3_2G032310' => 'csa', 'CsaV3_4G036880' => 'csa', 'CsaV3_5G003340' => 'csa', 'CSS0007768' => 'camsi', 'CSS0011395' => 'camsi', 'CSS0018766' => 'camsi', 'CSS0022894' => 'camsi', 'CSS0023100' => 'camsi', 'CSS0027913' => 'camsi', 'CSS0028774' => 'camsi', 'CSS0036644' => 'camsi', 'CSS0040209' => 'camsi', 'CSS0041684' => 'camsi', 'CSS0042236' => 'camsi', 'CSS0044960' => 'camsi', 'CSS0046972' => 'camsi', 'DCAR_005671' => 'dca', 'DCAR_006770' => 'dca', 'DCAR_008430' => 'dca', 'DCAR_008867' => 'dca', 'DCAR_017764' => 'dca', 'DCAR_020907' => 'dca', 'DCAR_022904' => 'dca', 'Dinv15888' => 'din', 'Dinv18153' => 'din', 'Dinv37702' => 'din', 'Dinv39030' => 'din', 'Dinv41423' => 'din', 'Dinv42913' => 'din', 'Dinv43187' => 'din', 'Duzib068G0101' => 'dzi', 'Duzib084G1012' => 'dzi', 'Duzib150G0628' => 'dzi', 'Duzib150G1394' => 'dzi', 'Duzib168G1603' => 'dzi', 'Duzib168G1729' => 'dzi', 'Duzib187G0559' => 'dzi', 'Duzib205G1139' => 'dzi', 'ECA246G0788' => 'eca', 'ECA246G4192' => 'eca', 'EL10Ac2g04154' => 'bvu', 'EL10Ac5g12711' => 'bvu', 'Eucgr.C00434' => 'egr', 'Eucgr.C01686' => 'egr', 'Eucgr.C02727' => 'egr', 'Eucgr.D01935' => 'egr', 'FAN04G1181' => 'fan', 'FAN08G2276' => 'fan', 'FAN13G2716' => 'fan', 'FAN15G2358' => 'fan', 'FAN18G1168' => 'fan', 'FAN19G1499' => 'fan', 'FAN20G1474' => 'fan', 'FAN23G2852' => 'fan', 'FAN24G3512' => 'fan', 'FAN26G1186' => 'fan', 'FAN27G1197' => 'fan', 'FAN28G0717' => 'fan', 'FvH4_1g01720' => 'fve', 'FvH4_2g28300' => 'fve', 'FvH4_3g16431' => 'fve', 'FvH4_3g43405' => 'fve', 'FvH4_5g01260' => 'fve', 'Glyma.01G214800' => 'gma', 'Glyma.04G064100' => 'gma', 'Glyma.05G050600' => 'gma', 'Glyma.06G065200' => 'gma', 'Glyma.09G095700' => 'gma', 'Glyma.11G027100' => 'gma', 'Glyma.13G157300' => 'gma', 'Glyma.14G112400' => 'gma', 'Glyma.14G114467' => 'gma', 'Glyma.15G202200' => 'gma', 'Glyma.17G104800' => 'gma', 'Glyma.17G132600' => 'gma', 'Glyma.17G215500' => 'gma', 'Glyma.18G083100' => 'gma', 'Gohir.A03G013500' => 'ghi', 'Gohir.A05G011300' => 'ghi', 'Gohir.A05G057000' => 'ghi', 'Gohir.A06G049900' => 'ghi', 'Gohir.A06G099900' => 'ghi', 'Gohir.A07G030300' => 'ghi', 'Gohir.A08G177500' => 'ghi', 'Gohir.A12G224000' => 'ghi', 'Gohir.A13G180600' => 'ghi', 'Gohir.D03G156100' => 'ghi', 'Gohir.D05G012000' => 'ghi', 'Gohir.D05G059100' => 'ghi', 'Gohir.D06G049200' => 'ghi', 'Gohir.D06G102100' => 'ghi', 'Gohir.D07G034100' => 'ghi', 'Gohir.D08G195900' => 'ghi', 'Gohir.D12G226700' => 'ghi', 'Gohir.D13G188500' => 'ghi', 'Gorai.001G035700' => 'gra', 'Gorai.003G163800' => 'gra', 'Gorai.004G206600' => 'gra', 'Gorai.008G242800' => 'gra', 'Gorai.009G012300' => 'gra', 'Gorai.009G060200' => 'gra', 'Gorai.010G056100' => 'gra', 'Gorai.010G117100' => 'gra', 'Gorai.013G213900' => 'gra', 'GSVIVG01012897001' => 'vvi', 'GSVIVG01019880001' => 'vvi', 'GSVIVG01035921001' => 'vvi', 'HanXRQChr02g0046741' => 'han', 'HanXRQChr02g0047341' => 'han', 'HanXRQChr02g0048661' => 'han', 'HanXRQChr02g0050251' => 'han', 'HanXRQChr03g0071911' => 'han', 'HanXRQChr05g0143261' => 'han', 'HanXRQChr06g0165171' => 'han', 'HanXRQChr13g0392011' => 'han', 'HanXRQChr13g0403111' => 'han', 'HanXRQChr13g0422701' => 'han', 'HanXRQChr14g0432811' => 'han', 'HanXRQChr16g0511121' => 'han', 'HanXRQChr17g0546361' => 'han', 'Haze_08979' => 'cav', 'Haze_19317' => 'cav', 'Haze_21458' => 'cav', 'Hma1.2p1_0138F.1_g062720' => 'hma', 'Hma1.2p1_0182F.1_g080510' => 'hma', 'Hma1.2p1_0371F.1_g138250' => 'hma', 'HPP92_000485' => 'vpl', 'HPP92_002966' => 'vpl', 'HPP92_017502' => 'vpl', 'HPP92_021724' => 'vpl', 'HPP92_021737' => 'vpl', 'HPP92_022214' => 'vpl', 'HPP92_022224' => 'vpl', 'Hund04456' => 'sun', 'Hund11534' => 'sun', 'Hund14709' => 'sun', 'Lalb_Chr05g0214751' => 'lal', 'Lalb_Chr07g0179521' => 'lal', 'Lalb_Chr08g0244271' => 'lal', 'Lalb_Chr09g0324701' => 'lal', 'Lalb_Chr11g0063611' => 'lal', 'Lalb_Chr11g0072861' => 'lal', 'Lalb_Chr16g0379961' => 'lal', 'Lalb_Chr24g0402061' => 'lal', 'Lj1g0023269' => 'lja', 'Lj2g0015468' => 'lja', 'Lj4g0025820' => 'lja', 'Lj6g0027679' => 'lja', 'Lj8C241G6' => 'lonja', 'Lj8C732G3' => 'lonja', 'Lj9A707G56' => 'lonja', 'Lsat_1_v5_gn_3_4341' => 'lsa', 'Lsat_1_v5_gn_4_9041' => 'lsa', 'Lsat_1_v5_gn_6_115500' => 'lsa', 'Lsat_1_v5_gn_6_12720' => 'lsa', 'Lsat_1_v5_gn_6_20120' => 'lsa', 'Lsat_1_v5_gn_8_63201' => 'lsa', 'Manes.02G030500' => 'mes', 'Manes.03G011800' => 'mes', 'Manes.06G041200' => 'mes', 'Manes.14G138700' => 'mes', 'Manes.16G126100' => 'mes', 'Mapoly0132s0008' => 'mpo', 'Mapoly0194s0001' => 'mpo', 'MBI04_g35059_MAGBIO' => 'mbi', 'MBI11_g32497_MAGBIO' => 'mbi', 'MBI14_g46656_MAGBIO' => 'mbi', 'MBI15_g03062_MAGBIO' => 'mbi', 'MD02G1012900' => 'mdo', 'MD04G1069700' => 'mdo', 'MD06G1071100' => 'mdo', 'MD08G1153600' => 'mdo', 'MD15G1130800' => 'mdo', 'MD15G1159800' => 'mdo', 'Medtr1g012960' => 'mtr', 'Medtr2g461240' => 'mtr', 'Medtr3g106400' => 'mtr', 'Medtr4g116545' => 'mtr', 'Medtr5g011070' => 'mtr', 'MELO3C005620.2' => 'cme', 'MELO3C011281.2' => 'cme', 'MELO3C016988.2' => 'cme', 'Migut.A00907' => 'egut', 'Migut.E01159' => 'egut', 'Migut.E01822' => 'egut', 'Migut.J01270' => 'egut', 'Migut.K00376' => 'egut', 'Migut.K00654' => 'egut', 'Migut.K00664' => 'egut', 'MSTRG.10637' => 'ama', 'MSTRG.10638' => 'ama', 'MSTRG.12028' => 'ama', 'MSTRG.13810' => 'ama', 'MSTRG.1904' => 'ama', 'MSTRG.19624' => 'ama', 'MSTRG.25566' => 'ama', 'MSTRG.26315' => 'ama', 'MSTRG.6093' => 'ama', 'Nitab4.5_0001021g0050' => 'nta', 'Nitab4.5_0001714g0080' => 'nta', 'Nitab4.5_0001751g0100' => 'nta', 'Nitab4.5_0002992g0080' => 'nta', 'Nitab4.5_0005330g0080' => 'nta', 'Nitab4.5_0008362g0020' => 'nta', 'Nitab4.5_0010572g0010' => 'nta', 'Nitab4.5_0011752g0030' => 'nta', 'Nitab4.5_0017496g0010' => 'nta', 'Nn1g01295' => 'nnu', 'Nn2g12249' => 'nnu', 'Nn6g34310' => 'nnu', 'Nn8g39719' => 'nnu', 'Oeu001901.1' => 'oeu', 'Oeu028741.1' => 'oeu', 'Oeu031588.1' => 'oeu', 'Oeu034998.1' => 'oeu', 'Oeu034999.1' => 'oeu', 'Oeu051703.2' => 'oeu', 'Oeu055915.1' => 'oeu', 'Oeu056765.1' => 'oeu', 'Oeu057291.1' => 'oeu', 'Oeu059051.3' => 'oeu', 'Os02g0182800' => 'osa', 'Os03g0123500' => 'osa', 'Os06g0646600' => 'osa', 'Os08g0292900' => 'osa', 'Peaxi162Scf00116g00083' => 'pax', 'Peaxi162Scf00620g00710' => 'pax', 'Peaxi162Scf01184g00135' => 'pax', 'Peaxi162Scf03709g00005' => 'pax', 'PGR031G1015' => 'pgr', 'PGR044G1766' => 'pgr', 'PGSC0003DMG400007887' => 'stu', 'PGSC0003DMG400015622' => 'stu', 'PGSC0003DMG400022736' => 'stu', 'PGSC0003DMG400030737' => 'stu', 'Phvul.002G153300' => 'pvu', 'Phvul.003G174900' => 'pvu', 'Phvul.003G213500' => 'pvu', 'Phvul.009G090500' => 'pvu', 'Phvul.009G209500' => 'pvu', 'Potri.001G112200' => 'ptr', 'Potri.006G190000' => 'ptr', 'Potri.006G259400' => 'ptr', 'Potri.018G022700' => 'ptr', 'Potri.018G114100' => 'ptr', 'Pp3c5_26440' => 'ppa', 'Pp3c6_1550' => 'ppa', 'Prupe.1G486200' => 'ppe', 'Prupe.5G088100' => 'ppe', 'Prupe.7G254700' => 'ppe', 'Psat0s149g0040' => 'psa', 'Psat2g181200' => 'psa', 'Psat4g033160' => 'psa', 'Psat5g030920' => 'psa', 'Psat6g028400' => 'psa', 'PSO017G0363' => 'pso', 'PSO017G6174' => 'pso', 'PSO170G5952' => 'pso', 'PSO478G1488' => 'pso', 'PSO782G0463' => 'pso', 'QL02p020199' => 'qlo', 'QL02p091335' => 'qlo', 'RcHm_v2.0_Chr2g0086661' => 'rch', 'RcHm_v2.0_Chr6g0297211' => 'rch', 'RcHm_v2.0_Chr7g0199751' => 'rch', 'Rhsim01G0049800' => 'rsi', 'Rhsim02G0205900' => 'rsi', 'Rhsim03G0254400' => 'rsi', 'Rhsim07G0096100' => 'rsi', 'Sabra01G0085700' => 'sbr', 'Sabra06G0146000' => 'sbr', 'Sabra18G0097000' => 'sbr', 'SalBow1G4508' => 'sbo', 'SalBow1G8588' => 'sbo', 'SalBow4G0593' => 'sbo', 'SalBow6G3061' => 'sbo', 'Sc01g0008860' => 'sci', 'Sc07g0009490' => 'sci', 'Sc09g0010360' => 'sci', 'Sc23g0006540' => 'sci', 'Sed0006996' => 'sed', 'Sed0018968' => 'sed', 'Sed0019443' => 'sed', 'Sed0024191' => 'sed', 'Sed0025103' => 'sed', 'Sed0026276' => 'sed', 'SEGI_17468' => 'sgi', 'SEGI_18120' => 'sgi', 'SGA_v2.0_scaffold144G35977' => 'sas', 'SGA_v2.0_scaffold196G40902' => 'sas', 'SGA_v2.0_scaffold20G09082' => 'sas', 'SGA_v2.0_scaffold286G47124' => 'sas', 'SGA_v2.0_scaffold546G52831' => 'sas', 'SGA_v2.0_scaffold64G21996' => 'sas', 'SHI18504' => 'shi', 'SMO118G0426' => 'smo', 'SMO223G0041' => 'smo', 'Solyc07g007120.3' => 'sly', 'Solyc08g041820.3' => 'sly', 'Solyc08g080120.3' => 'sly', 'Solyc12g010410.3' => 'sly', 'Sopen07g003170' => 'spe', 'Sopen08g012000' => 'spe', 'Sopen08g028480' => 'spe', 'Sopen12g005430' => 'spe', 'Sp2g01590' => 'spa', 'Sp2g22310' => 'spa', 'Sp6g32440' => 'spa', 'Sp7g29840' => 'spa', 'TAR375G0440' => 'tar', 'TAR383G0568' => 'tar', 'TAR418G0004' => 'tar', 'TAR614G0001' => 'tar', 'TAR625G0821' => 'tar', 'TAR626G0978' => 'tar', 'TAR633G2609' => 'tar', 'TAR636G0657' => 'tar', 'TAR636G2036' => 'tar', 'THA.LOC104799035' => 'tha', 'THA.LOC104803641' => 'tha', 'THA.LOC104809431' => 'tha', 'THA.LOC104815008' => 'tha', 'Thecc.03G268600' => 'tca', 'Thecc.09G019600' => 'tca', 'Thecc.09G141900' => 'tca', 'Thhalv10004250m.g' => 'esa', 'Thhalv10013773m.g' => 'esa', 'Thhalv10023617m.g' => 'esa', 'Thhalv10025443m.g' => 'esa', 'TPR.G15782' => 'tpr', 'TPR.G19592' => 'tpr', 'TPR.G3150' => 'tpr', 'TPR.G38896' => 'tpr', 'TWI15G0886' => 'twi', 'TWI32G0282' => 'twi', 'TWI34G1381' => 'twi', 'TWI60G1397' => 'twi', 'TWI63G0121' => 'twi', 'TWI63G0156' => 'twi', 'TWI81G0254' => 'twi', 'unitig_0.g2705' => 'ugi', 'unitig_26.g9690' => 'ugi', 'unitig_46.g18386' => 'ugi', 'unitig_72.g29743' => 'ugi', 'unitig_72.g29744' => 'ugi', 'unitig_746.g26538' => 'ugi', 'unitig_748.g7180' => 'ugi', 'unitig_749.g13408' => 'ugi', 'vmacro06108' => 'vma', 'vmacro11213' => 'vma', 'vmacro14011' => 'vma', 'vmacro21881' => 'vma', 'vmacro22577' => 'vma', 'VMungo0331G0420' => 'vmu', 'VMungo1215G0046' => 'vmu', 'VMungo1215G1876' => 'vmu', 'VMungo1215G3335' => 'vmu', 'VMungo1309G1499' => 'vmu', 'VMungo1309G2292' => 'vmu', 'Zm00001eb001720' => 'zma', 'Zm00001eb206760' => 'zma', 'Zm00001eb234270' => 'zma', 'Zm00001eb386830' => 'zma', 'Zm00001eb403720' => 'zma' ) $gf_id = 'HOM05D001212' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001212' ) $data_identifier = 'HOM05D001212' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 14, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 9, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 10, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403720' $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